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[(que)12.8(nce)11.7(s)-294.6(tha)12.7(t)-300.7(wer)12(e)-296(gen)12.8(era)11.7(ted)-292.6(in)-290.3(hig)13.8(h)-300.6(thr)13.9(oug)14(hp)15.1(ut)-296.1(at)-297.2(the)-286.8(Wel)10.4(l-)]TJ
0 -1.1116 TD
[(com)11.6(e)-278.7(Tru)12.8(st)-272.8(San)13(ger)-275.1(Ins)14.2(tit)19.4(ute)-275.3(on)-272.9(the)]TJ
/F5 1 Tf
14.1574 0 TD
[(Ill)13.8(umi)13(na)-278.7(Mi)13.9(Seq)]TJ
/F4 1 Tf
6.4682 0 TD
[(pla)18.5(tfo)13.9(rm,)]TJ
-20.6255 -1.1116 TD
[(aft)12.7(er)-412.3(aut)12.7(oma)17.3(ted)-407.8(ext)12.7(rac)11.7(tio)13.7(n)-415.8(o)0(f)-411.1(vir)13.9(al)-412.4(RNA)-409.3(an)13.9(d)-415.8(amp)11.6(li)13.9(cat)11.5(ion)]TJ
0 -1.1174 TD
[(wit)12.8(h)-266(a)-261.4(uni)13.8(ver)12.8(sal)-257.8(HIV)12.3(-1)-261.4(pri)13.9(me)12.7(r)-266(set)12.9(.)]TJ
7.3823 0 0 6.5614 197.4614 280.233 Tm
(10)Tj
9.843 0 0 9.843 207.3826 275.8109 Tm
[(The)-259.1(seq)13(uen)12.8(ce)12.8(s)-265.9(are)-259(fro)14(m)]TJ
-14.7679 -1.1116 TD
[(div)13.8(ers)13(e)-347.8(set)12.9(tin)13.7(gs)-347.6(in)-342.1(sub)14.2(-Sa)13(har)12.8(an)-343.2(Afr)13.2(ica)11.5(,)-349(i)0(n)15(clu)12.7(din)13.8(g)-352.4(c)0(o)13.9(hor)14(ts)-347.7(of)]TJ
T*
[(the)-425(gen)12.8(era)11.7(l)-433.2(pop)14(ula)12.7(tio)13.7(n)-433.1(a)0(t)-429.7(var)12.8(iou)13.8(s)-432.9(sur)14.2(vei)12.7(lla)12.6(nce)-426.1(sit)13.9(es)-429.4(\(Ra)11.8(kai)]TJ
T*
[(Com)11.7(mun)18.5(ity)-769.6(Coh)12.9(ort)-769.4(Stu)14(dy,)]TJ
7.3823 0 0 6.5614 176.4283 247.3511 Tm
(11)Tj
9.843 0 0 9.843 191.3952 242.9858 Tm
[(Moc)11.9(hud)14(i)-778.8(Pre)13(ven)12.8(tio)13.7(n)-778.7(Pro)14.2(-)]TJ
-13.1436 -1.1174 TD
[(jec)11.5(t,)]TJ
7.3823 0 0 6.5614 78.5764 236.3527 Tm
[(12,1)22.1(3)]TJ
9.843 0 0 9.843 98.022 231.9873 Tm
[(MR)13.1(C/U)11.9(VRI)-293.2(Uga)11.9(nda)-292.4(gen)12.8(er)14(al)-297.2(pop)14(ula)12.7(tio)13.7(n)-300.6(and)-292.4(sh)14.3(er-)]TJ
-3.6574 -1.1116 TD
[(fol)13.9(k)-438.8(coh)12.8(ort)13.9(s)]TJ
7.3823 0 0 6.5614 110.7779 225.411 Tm
[(14)17.8(16)]TJ
9.843 0 0 9.843 129.033 221.0456 Tm
[(\),)-436.5(a)-440(coh)12.8(ort)-429.6(of)-439.9(fem)17.4(ale)-432(sex)13(-wo)13.1(rke)12.8(rs)-439.7(\()-75.9(MRC)11(/)]TJ
-6.808 -1.1116 TD
[(UVR)11.2(I)-490.6(Uga)11.9(nda)-482.5(Goo)13.1(d)-490.7(Hea)10.8(lth)-481.6(for)-481.3(Wom)16.2(en)]TJ
7.3823 0 0 6.5614 230.6834 214.4692 Tm
(17)Tj
9.843 0 0 9.843 237.9968 210.1039 Tm
[(\),)-488.3(his)14(tor)13.9(ica)11.5(l)-490.8(se-)]TJ
-17.8781 -1.1174 TD
[(que)12.8(nce)11.7(s)-225.5(fro)14(m)-226.9(the)-217.7(198)14(0s,)-218.5(and)-217.6(a)-226.9(coh)12.8(ort)-222.3(of)-221(HIV)12.3(-1)-221(dru)14(g-r)14(esi)12.9(sta)12.9(nt)]TJ
0 -1.1116 TD
[(ind)13.8(ivi)13.7(dua)12.8(ls)-451.4(fro)14(m)-451.6(nor)14(the)12.7(rn)-451.4(Kw)13.3(aZu)11.6(lu-)13.9(Nat)11.8(al)-452.7(in)-445.8(Sou)14.1(th)-451.6(Afr)13.2(ica)]TJ
T*
[(\(Af)13.2(ric)12.7(a)-273(Hea)10.8(lth)-268.5(Res)12(ea)12.8(rch)-269.4(Ins)14.2(tit)13.6(ute)-263.8(Res)12(ist)13.9(anc)11.7(e)-278.7(C)0(o)14(hor)14(t)]TJ
7.3823 0 0 6.5614 266.6267 181.5874 Tm
(18)Tj
9.843 0 0 9.843 273.9401 177.222 Tm
(\).)Tj
-20.5161 -1.1174 TD
[(Most)-339.3(PANGEA-HIV)-339.8(consensus)-340(sequences)-342.5(from)-339.6(Botswa-)]TJ
-1.0137 -1.1116 TD
[(na,)-312.1(South)-310.7(Africa,)-312.8(and)-309.7(MRC/UVRI)-314.2(Uganda)-315.1(cover)-307.3(nearly)-314.3(the)]TJ
T*
[(entire)-343.2(viral)-346.7(genome)-344.2(from)-345.4(the)]TJ
/F5 1 Tf
12.2048 0 TD
(gag)Tj
/F4 1 Tf
1.8431 0 TD
(to)Tj
/F5 1 Tf
1.1231 0 TD
(nef)Tj
/F4 1 Tf
1.5666 0 TD
[(genes.)-345.1(Sequencing)]TJ
-16.7377 -1.1116 TD
[(success)-315.9(rates)-307.2(were)-312.8(considerably)-310.5(lower)-312.9(for)-308.5(samples)-310.5(from)-310.8(the)]TJ
0 -1.1174 TD
[(Rakai)-233.6(Community)-232.5(Cohort)-232.4(and)-229.1(varied)-233.7(substantially)-235.8(across)-233.1(the)]TJ
0 -1.1116 TD
[(genome.)-238.2(Potential)-237.2(reasons)-240(for)-239.4(variation)-237.2(in)-232.7(NGS)-241(success)-235.2(rates)]TJ
T*
[(could)-185.3(be)-181.9(as)-187.5(follows:)-182.6(low)-182.8(viral)-185.4(RNA)-184.6(count)-185.4(at)-182(time)-185.6(of)-180.7(sampling;)]TJ
0 -1.1174 TD
[(sample)-229(degradation)-234.7(before)-227.7(RNA)-230.7(extraction;)-235(failure)-229.1(to)-227(extract)]TJ
0 -1.1116 TD
[(viral)-248.8(RNA)-253.7(from)-247.5(plasma)-246.2(or)-249.8(serum)-249.6(samples;)-254.1(failure)-246.4(to)-250(amplify)]TJ
T*
[(extracted)-464(RNA)-466.9(with)-460.5(the)-459.6(universal)-467.3(HIV-1)-462.2(primer)-464.1(set;)-460.6(and)]TJ
0 -1.1174 TD
[(failure)-298.2(during)-294.7(sequencing)-296.7(or)-290.2(sequence)-295.5(assembly.)-297.8(Our)-297.9(inves-)]TJ
25.504 46.7631 TD
[(tigations)-190(below)-186.2(indicate)-191.2(that)-184.4(a)-186.6(number)-187.5(of)-186.5(factors,)-191.9(and)-183(not)-187.7(only)]TJ
0 -1.1116 TD
[(low)-332.6(serum/plasma)-330(HIV-1)-329.7(RNA)-328.6(loads,)-332.6(were)-330.1(associated)-332.3(with)]TJ
T*
[(partial)-286.9(sequencing)-285.2(failure.)]TJ
1.0137 -1.1174 TD
[(Phylogenomic)-276.1(studies)-267.9(across)-273.5(the)-269.5(tree)-271.8(of)-272.9(life)-270.7(highlight)-269.6(that)]TJ
-1.0137 -1.1116 TD
[(phylogenies)-262.2(can)-264.8(be)-256.8(accurately)-264.7(reconstructed)-266.6(from)-259(sequences)]TJ
T*
[(with)-345.4(very)-345.4(high)-344.4(proportions)-346.2(of)-342(missing)-342.9(characters.)]TJ
7.3823 0 0 6.5614 512.7872 466.5258 Tm
(1925)Tj
9.843 0 0 9.843 534.6707 462.1605 Tm
(This)Tj
-22.5147 -1.1174 TD
[(could)-404.2(also)-402.9(be)-406.5(the)-402(case)-405.1(for)-400.7(HIV-1)-404.6(phylogenies.)-403.8(Longer)-400.6(se-)]TJ
0 -1.1116 TD
[(quenc)-7.8(es)-435.2(of)-439.9(HIV-1)-439.2(genomes)-437.3(increase)-445.3(phylogenetic)-437.6(accura-)]TJ
T*
(cy,)Tj
7.3823 0 0 6.5614 324.8503 433.644 Tm
[(26,)-9.4(27)]TJ
9.843 0 0 9.843 344.6928 429.2786 Tm
[(because)-329(more)-323.6(nucleotide)-325.9(characters)-327.7(are)-322.4(available)-326(to)]TJ
-3.2139 -1.1174 TD
[(resolve)-194.2(internal)-190(branches)-196.4(through)-186.4(characters)-195.3(that)-190.1(are)-189.9(uniquely)]TJ
0 -1.1116 TD
[(shared)-348.5(among)-347.7(sets)-345.1(of)-347.7(sequences,)-351.7(and)-344.3(to)-342.1(infer)-346.6(multiple)-351.5(sub-)]TJ
T*
[(stitutions)-287.7(between)-282.9(convergent)-285.3(sequences.)]TJ
7.3823 0 0 6.5614 476.844 400.7621 Tm
(28)Tj
9.843 0 0 9.843 323.0361 385.455 Tm
[(On)-268(the)-263.8(contrary,)-268.1(and)-263.7(similar)-269.5(to)-267.3(many)-266(other)-266(pathogens,)-269(the)]TJ
-1.0137 -1.1174 TD
[(HIV-1)-496.8(genome)-499.7(is)-491.7(short)-495(\(9,719)-164.4(nt)-497.7(for)-492.8(the)-494.2(reference)-499.4(strain)]TJ
0 -1.1116 TD
[(HXB2,)-575.1(including)-575.9(5)]TJ
/F6 1 Tf
8.294 0 TD
()Tj
/F4 1 Tf
.2534 0 TD
[(-)-571.3(and)-574.7(3)]TJ
/F6 1 Tf
3.4213 0 TD
()Tj
/F4 1 Tf
.2534 0 TD
[(-LTR)-572.3(sequences\).)-577.4(Thus,)-579(the)]TJ
-12.2221 -1.1116 TD
[(number)-682.9(of)-676.1(informative)-678.4(characters)-684.8(between)-680.3(full-genome)]TJ
0 -1.1174 TD
[(HIV-1)-370(sequences)-371.3(remains)-368.3(limited,)-371.2(and)-367.3(missing)-365.9(data)-364(act)-368.6(by)]TJ
0 -1.1116 TD
[(reducing)-402.9(the)-396.2(number)-400.6(of)-399.6(shared)-394.6(informative)-401.9(characters)-408.4(dis-)]TJ
T*
[(propor)-6.5(tionally)-327.3(when)-329(any)-332.8(two)-326.8(sequences)-336.7(have)-329.3(missing)-331.4(char-)]TJ
0 -1.1174 TD
[(acters)-286.5(at)-280(different)-283.1(alignment)-284.6(positions.)]TJ
1.0137 -1.1116 TD
[(In)-555.1(addition,)-549.5(HIV-1)-554.4(phylogenies)-555.9(from)-552.7(generalized)-559.6(epi-)]TJ
-1.0137 -1.1116 TD
[(demics)-401.8(in)-399.7(sub-Saharan)-401.1(Africa)-401.5(are)-397.3(broad)-398.3(and)-396.1(exhibit)-400.9(many)]TJ
0 -1.1174 TD
[(long)-309.8(branches.)]TJ
7.3823 0 0 6.5614 371.1684 280.233 Tm
(12,29,30)Tj
9.843 0 0 9.843 400.0251 275.8109 Tm
[(Indeed,)-311.8(due)-304(to)-307.6(the)-304.1(sheer)-307.1(magnitude)-307.5(of)]TJ
-8.8354 -1.1116 TD
[(generalize)-11.3(d)-260.3(HIV-1)-272.1(epidemics)-268.1(in)-267.3(sub-Saharan)-268.6(Africa,)-266.7(closely)]TJ
T*
[(related)-570.1(sequences)-561.4(are)-564.3(often)-565.5(not)-562.1(available)-562.1(to)-561(break)-566.5(long)]TJ
T*
[(branches)-374.9(in)-370.9(viral)-375.5(phylogenies,)]TJ
7.3823 0 0 6.5614 435.0613 247.3511 Tm
(31)Tj
9.843 0 0 9.843 446.1164 242.9858 Tm
[(although)-373.1(other)-369.6(factors,)-370.4(in-)]TJ
-13.518 -1.1174 TD
[(cluding)-239.5(onward)-239(transmission)-240(months)-238.2(or)-238.3(years)-238(after)-238.3(infection,)]TJ
0 -1.1116 TD
[(also)-443.2(contribute)-439.9(to)-440.1(the)-442.3(presence)-439.5(of)-439.9(long)-436.5(branches.)]TJ
7.3823 0 0 6.5614 516.8691 225.411 Tm
(32)Tj
9.843 0 0 9.843 528.6046 221.0456 Tm
(When)Tj
-21.8984 -1.1116 TD
[(branches)-455.6(are)-449.1(long,)-445.7(more)-450.3(informative)-453.7(sites)-450(are)-449.1(required)-448.9(to)]TJ
0 -1.1174 TD
[(correctly)-341.9(infer)-340.8(phylogenetic)-339.6(relationships,)-342.7(and)-338.5(missing)-337.1(data)]TJ
0 -1.1116 TD
[(could)-214.1(in)-209.7(this)-211.8(context)-211.9(indirectly)-209.7(exacerbate)-219.7(tree)-208.4(reconstruction)]TJ
T*
(artifacts.)Tj
7.3823 0 0 6.5614 347.4141 181.5874 Tm
[(31,)-9.4(33,34)]TJ
9.843 0 0 9.843 377.9716 177.222 Tm
[(These)-475.4(considerations)-473.9(suggest)-475.2(that)-472.4(missing)]TJ
-6.5949 -1.1174 TD
[(data)-364(in)-365.2(HIV-1)-364.3(sequences)-365.5(could)-363.9(have)-363.8(a)-359.4(substantial)-371.7(negative)]TJ
0 -1.1116 TD
[(impact)-321.5(on)-319(tree)-317.9(reconstruction)-324.3(accuracy)-319.9(and)-315.5(subsequent)-324.1(mo-)]TJ
T*
[(lecular)-466.4(epidemiological)-460.8(studies,)-461.4(especially)-465.1(in)-457.3(sub-Saharan)]TJ
T*
[(African)-287.4(settings)-280.7(where)-285.1(sequence)-284(sampling)-282(is)-284.4(limited.)]TJ
1.0137 -1.1174 TD
[(To)-694.6(characterize)-695.4(the)-690(implications)-696.9(of)-693.3(missing)-688.5(nucleo-)]TJ
-1.0137 -1.1116 TD
[(tide)-380.2(characters)-385.3(in)-376.7(PANGEA-HIV)-385.8(sequences)-382.8(on)-376.6(tree)-381.2(recon-)]TJ
T*
[(struction)-535.4(accuracy,)-536.4(we)-528.4(conducted)-531.9(simulation)-532.1(studies.)-530.6(An)]TJ
0 -1.1174 TD
[(individual-level)-620.9(transmission)-614.4(and)-615(prevention)-612.6(model)-612.8(was)]TJ
0 -1.1116 TD
[(used)-408.6(to)-405.5(generate)-411(regional)-408.8(HIV-1)-410.4(epidemics)-412.1(in)-405.5(populations)]TJ
T*
(of)Tj
/F9 1 Tf
1.3017 0 TD
(*)Tj
/F4 1 Tf
1.0022 0 TD
[(80,000)-464(individuals,)-472.1(as)-469.7(well)-467.5(as)-469.7(corresponding)-471.5(HIV-1)]TJ
-2.3039 -1.1174 TD
[(phylogenies)-429.2(and)-424.9(full-genome)-424.8(sequences.)]TJ
7.3823 0 0 6.5614 478.2613 61.0583 Tm
(35)Tj
9.843 0 0 9.843 489.77 56.6362 Tm
[(Each)-428.4(simulated)]TJ
/F1 1 Tf
8.9663 0 0 8.9663 62.022 749.6502 Tm
(1084)Tj
46.0624 0 TD
[(RATMANN)-337.5(ET)-338.7(AL.)]TJ
ET
endstream
endobj
66 0 obj
<>stream
/GS1 gs
BT
/F4 1 Tf
9.843 0 0 9.843 59.7543 725.1588 Tm
0 0 0 rg
0 Tc
0 Tw
[(sequence)-410.7(was)-402.6(paired)-406.5(at)-400.9(random)-406.4(with)-403(a)-399.7(PANGEA-HIV)-408.9(se-)]TJ
0 -1.1174 TD
[(quence,)-387.9(and)-378.8(missing)-389(nucleotide)-383.5(patterns)-385.5(of)-382.3(PANGEA-HIV)]TJ
0 -1.1116 TD
[(sequences)-256.1(were)-249.5(superimposed)-252.6(onto)-246.4(the)-252.3(simulated)-249.8(sequences.)]TJ
T*
[(We)-524(then)-518.3(tested)-521.6(several)-523.7(tree)-525.2(reconstruction)-525.9(tools)-518.2(in)-520.7(their)]TJ
T*
[(ability)-395.3(to)-394(re-estimate)-392.5(known)-392.3(HIV-1)-393.1(phylogenies)-394.7(from)-397.2(par-)]TJ
0 -1.1174 TD
[(tially)-284.7(determined)-286.7(consensus)-282.4(sequences.)]TJ
1.0137 -1.1116 TD
[(These)-509.9(analyses)-513.1(provide)-510.1(insight)-503.2(into)-511.5(the)-505.7(accuracy)-515.7(with)]TJ
-1.0137 -1.1116 TD
[(which)-324.5(viral)-329.4(phylogenetic)-322.4(relationships)-327.8(can)-328.2(be)-320.1(reconstructed)]TJ
0 -1.1174 TD
[(from)-247.5(NGS)-246.8(that)-247.7(have)-242.9(missing)-250.7(characters)-247.1(at)-245.4(different)-248.6(positions)]TJ
0 -1.1116 TD
[(in)-428.5(the)-430.8(sequence)-433.7(alignment.)-432(Since)-428.3(all)-430.9(molecular)-435.3(epidemio-)]TJ
T*
[(logical)-344.5(investigations)-340.6(rely)-339.7(on)-336.3(accur)-9(ately)-336.4(reconstructed)-347.3(viral)]TJ
0 -1.1174 TD
[(phylogenies,)-248.3(our)-245.2(ndings)-249.4(are)-241.7(fundamental)-253.2(to)-244.2(PANGEA-HIV)]TJ
0 -1.1116 TD
[(and)-280.9(analogous)-282.9(full-genome)-286.6(viral)-283.4(sequencing)-285.2(efforts.)]TJ
/F1 1 Tf
8.9663 0 0 8.9663 59.7543 568.9132 Tm
[(Materials)-339(and)-331.9(Methods)]TJ
/F10 1 Tf
0 -1.8273 TD
[(Next-generation)-336.8(sequencing)]TJ
/F4 1 Tf
9.843 0 0 9.843 69.7323 536.088 Tm
[(Serum)-359(and)-355.8(plasma)-361.4(samples)-362.3(from)-356.9(PANGEA-HIV)-362.8(partici-)]TJ
-1.0137 -1.1174 TD
[(pating)-261.5(cohort)-255.5(sites)-260(in)-255.8(Uganda)-257.5(and)-257.9(Botswana)-254.9(were)-261(shipped)-256.5(to)]TJ
0 -1.1116 TD
[(University)-295.4(College)-293.6(Londo)-6.7(n)-289.1(Hospital,)-290.9(London,)-293.5(United)-296.9(King-)]TJ
T*
[(dom,)-313.2(for)-308.5(automated)-314.4(RNA)-311.3(sample)-309.6(extraction)-314.4(on)-307.5(QIAsymph-)]TJ
0 -1.1174 TD
[(ony)-475.6(SP)-468.4(workstations)-476(with)-472.1(the)-476.9(QIAsymphony)-469.9(DSP)-476.1(Virus/)]TJ
0 -1.1116 TD
[(Pathogen)-460.4(Kit)-453.7(\(Cat.)-453.6(No.)-455.8(937036,)-453.5(937055;)-457.1(Qiagen,)-456.9(Hilden,)]TJ
T*
[(Germany\),)-327.6(followed)-327.9(by)-319(one-step)-327.8(reverse)-327.7(transcription)-327.9(poly-)]TJ
0 -1.1174 TD
[(merase)-569.8(chain)-566.7(reaction)-571.2(\(RT-PCR\))-571.6(as)-561.9(described)-572(in)-566.8(Ref.)]TJ
7.3823 0 0 6.5614 291.4582 463.7479 Tm
(10)Tj
9.843 0 0 9.843 59.7543 448.3842 Tm
[(Amplication)-283(was)-275.9(assessed)-276.5(through)-272.8(gel)-275.3(electrophoresis)-280.3(on)-272.9(a)]TJ
0 -1.1116 TD
[(fraction)-316.6(of)-313.2(samples,)-313.9(and)-315.5(samples)-316.3(were)-312.8(shipped)-314.1(to)-313.3(the)-315.6(Well-)]TJ
T*
[(come)-284.4(Trust)-283.1(Sanger)-279.4(Institute,)-285.5(Hinxton,)-283(United)-279.6(Kingdom.)]TJ
1.0137 -1.1174 TD
[(From)-425.9(plasma)-430.6(samples)-431.5(from)-426(the)-430.8(resistance)-430.2(cohort,)-426(RNA)]TJ
-1.0137 -1.1116 TD
[(was)-517.8(extracted)-515.9(at)-516.1(the)-511.4(Africa)-516.7(Health)-516.9(Research)-521.1(Institute)-512.5(in)]TJ
T*
[(Durban,)-219.4(South)-218.6(Africa,)-220.7(using)-218.5(the)-217.7(QIAamp)-218.1(Viral)-215.1(Mini)-218.7(kit)-216.7(\(Cat.)]TJ
0 -1.1174 TD
[(No)-406.3(52906;)-404.2(Qiagen\),)-411.9(followed)-408.5(by)-405.4(one-step)-402.7(RT-PCR)-408.1(as)-406.3(de-)]TJ
0 -1.1116 TD
[(scribed)-407.4(in)-399.7(Ref.)]TJ
7.3823 0 0 6.5614 120.5858 376.044 Tm
(10)Tj
9.843 0 0 9.843 131.9244 371.6786 Tm
[(Amplicons)-404.9(were)-399.2(puried)-406.2(using)-402.9(the)-402(QIA-)]TJ
-7.3321 -1.1116 TD
[(quick)-289(Purication)-290.9(kit)-291.5(\(Cat.)-286.6(No.)-288.7(28106;)-289(Qiagen\))-293.2(and)-286.7(shipped)]TJ
0 -1.1174 TD
[(to)-284.6(the)-281.1(Wellcome)-281(Trust)-283.1(Sanger)-285.2(Institute.)]TJ
1.0137 -1.1116 TD
[(Next-generation)-442.8(se)19.9(qu)20.8(en)19.7(ci)19.5(ng)-411.1(wa)18.8(s)-427.1(p)0(e)19.7(r)0(f)20.9(o)0(r)20.9(m)0(e)18.4(d)-421.6(as)-412.1(de)13.9(sc)19.9(ri)20.7(be)19.7(d)]TJ
-1.0137 -1.1116 TD
[(pr)15.1(ev)19.7(io)20.7(us)21(ly)-278.8(on)-272.9(th)20.7(e)]TJ
/F5 1 Tf
7.1996 0 TD
[(Il)20.7(lu)20.7(mi)14.1(na)-272.9(Mi)19.6(Se)19.7(q)]TJ
/F4 1 Tf
6.4221 0 TD
[(pl)20.7(at)19.5(fo)20.9(rm)-279.9(in)-273(th)15(e)-284.5(D)0(N)19.1(A)-289.9(pi)20.7(pe)19.7(-)]TJ
-13.6217 -1.1174 TD
[(li)14.8(ne)19.7(s)-265.8(c)0(o)13.9(r)0(e)-256.8(f)0(a)19.7(c)0(i)13.8(l)0(i)20.6(t)0(y)-255.8(a)0(t)-262.7(t)0(h)20.7(e)-273(We)17.4(ll)20.6(co)19.7(me)-263.8(Tr)19.7(us)21(t)-271.9(S)0(a)19.8(n)0(g)20.8(e)0(r)-262.5(I)0(n)20.9(s)0(t)20.9(i)0(t)20.6(u)0(t)20.7(e)0(.)]TJ
7.3823 0 0 6.5614 283.5779 321.2787 Tm
(36)Tj
/F10 1 Tf
8.9663 0 0 8.9663 59.7543 292.1952 Tm
[(HIV-1)-339.6(consensus)-330(sequences)]TJ
/F4 1 Tf
9.843 0 0 9.843 69.7323 275.7543 Tm
[(N)-7.7(e)0(x)-9.1(t)-7(-)-6.8(g)0(e)-9.1(n)-6.9(er)-9.1(a)-8(t)0(i)-8.2(o)-6.9(n)-392.8(s)-6.7(eq)-9.1(u)-6.9(e)0(n)-9.1(c)-8(in)-8.1(g)-392.8(o)-6.9(u)-6.9(t)0(p)-8.1(u)-6.9(t)-392.9(w)-7.7(as)-394.8(a)-8(s)-6.7(s)-6.7(e)0(m)-10.3(b)0(l)-8.1(e)-8(d)-392.8(w)-7.7(it)-8.2(h)]TJ
-1.0137 -1.1116 TD
[(t)-7(h)-6.9(e)-428.5(S)-6.7(HI)-8.8(V)-7.7(E)0(R)-436.4(s)0(e)-8.9(q)-6.9(ue)-9.1(n)-6.9(c)0(e)-436.5(a)0(s)-8.9(s)-6.7(em)-10.3(b)-6.9(l)0(y)-434.3(p)0(i)-8.1(p)-6.9(el)-9.3(i)-7(n)0(e)-9.1(.)]TJ
7.3823 0 0 6.5614 232.9511 269.1779 Tm
(37)Tj
9.843 0 0 9.843 244.6298 264.8125 Tm
.0072 Tc
[(Bri)7.2(e)-2(y)7.2(,)-423.5(s).5(ho)7.2(rt)]TJ
-18.7824 -1.1174 TD
0 Tc
[(r)-6.8(e)-8(ad)-9.1(s)-242.8(w)-7.7(e)-8(r)0(e)-251(m)0(a)-10.4(p)-6.9(pe)-9.1(d)-243(t)-7(o)-243(a)]TJ
/F5 1 Tf
9.7569 0 TD
.0076 Tc
[(de)-236.6(no)7.6(vo)]TJ
/F4 1 Tf
3.404 0 TD
0 Tc
[(r)-6.8(e)-8(fe)-9.1(r)-6.8(e)-8(nc)-9.1(e)-244.2(c)-8(on)-8(s)-6.7(t)-7(ru)-7.9(c)-8(t)0(e)-9.2(d)-243(u)-6.9(s)-6.7(in)-8.1(g)]TJ
-13.1609 -1.1116 TD
[(c)-8(o)-6.9(nt)-8.1(i)-7(g)-6.9(s)-519.3(\()-6.8(th)-8.1(a)-8(t)-519.6(w)-7.7(e)0(r)-9.1(e)-520.6(a)-8(s)-6.7(se)-8.9(m)-8.1(b)0(l)-8.1(e)-8(d)-519.5(f)-6.8(ro)-7.9(m)-520.7(t)-7(h)-6.9(e)-520.6(s)-6.7(h)0(o)-8(r)-6.8(t)-519.6(r)-6.8(ea)-10.3(d)-6.9(s)-519.3(w)-7.7(i)0(t)-8.2(h)]TJ
T*
.0073 Tc
(IVA)Tj
7.3823 0 0 6.5614 77.3291 236.296 Tm
.0145 Tc
(38)Tj
9.843 0 0 9.843 84.8693 231.9306 Tm
0 Tc
[(\))-392.7(a)0(n)-9.1(d)-392.8(a)-393.9(s)-6.7(et)-395.1(o)-6.9(f)-392.7(s)-6.7(t)0(a)-9.2(n)-6.9(d)-6.9(a)0(r)-9.1(d)-392.8(w)-7.7(h)0(o)-8(l)-7(e-)-9.1(g)-6.9(e)0(n)-9.1(o)-6.9(me)-396.3(r)-6.8(e)-8(fe)-9.1(r)-6.8(e)0(n)-9.1(c)-8(e)-393.9(s)0(e)-8.9(-)]TJ
-2.5516 -1.1174 TD
.0076 Tc
[(que)7.6(nce)7.6(s)-1.3(.)]TJ
7.3823 0 0 6.5614 94.3937 225.3543 Tm
.0145 Tc
(39)Tj
9.843 0 0 9.843 104.7685 220.9322 Tm
0 Tc
[(U)-7.7(s)-6.7(in)-8.1(g)-6.9(,)-297.2(wh)-8.8(e)-8(r)0(e)-297.1(a)-8(v)-6.9(a)0(i)-9.2(l)-7(a)-8(b)0(l)-8.1(e)-8(,)-291.4(t)-7(h)-6.9(e)-296(c)-8(o)0(n)-8(t)-7(ig)-8.1(s)-294.6(f)-6.8(o)-6.9(r)-294.8(m)-8.1(a)0(p)-9.1(p)-6.9(in)-8.1(g)]TJ
-4.5732 -1.1116 TD
[(i)-7(n)-6.9(cr)-9.1(e)-8(a)0(s)-8.9(e)-8(d)-323.6(a)-8(c)-8(c)0(u)-9.1(r)-6.8(ac)-10.3(y)-323.6(i)-7(n)-323.6(t)-7(h)-6.9(e)-324.8(c)-8(o)0(n)-8(s)-6.7(t)-7(r)0(u)-7.9(c)-8(te)-9.2(d)-323.6(c)-8(o)-6.9(n)0(s)-7.8(e)-8(n)-6.9(s)0(u)-7.8(s)-329.2(se)-8.9(q)-6.9(u)0(e)-9.1(n)-6.9(ce)-10.3(s)]TJ
T*
[(c)-8(o)-6.9(mp)-9.2(a)-8(r)0(e)-9.1(d)-214.2(to)-215.4(u)-6.9(s)-6.7(in)-8.1(g)-214.2(s)-6.7(ta)-9.2(n)-6.9(d)0(a)-9.1(r)-6.8(d)-214.2(r)0(e)-9.1(f)-6.8(er)-9.1(e)-8(n)0(c)-9.1(e)-215.4(s)-6.7(e)0(q)-9.1(u)-6.9(en)-9.1(c)-8(e)0(s)-216.3(a)-8(l)-7(o)0(n)-8(e)-8(.)-210.8(G)-7.7(a)0(p)-9.1(s)]TJ
0 -1.1174 TD
[(b)-6.9(e)-8(tw)-9(e)-8(e)0(n)-331.7(c)-8(o)-6.9(n)0(t)-8.1(i)-7(gs)-330.3(i)-7(n)-329.4(t)-7(h)0(e)-331.7(r)-6.8(e)-8(f)0(e)-9.1(r)-6.8(en)-9.1(c)-8(e)-330.6(se)-8.9(q)-6.9(u)-6.9(e)0(n)-9.1(c)0(e)-332.8(w)-7.7(e)-8(r)0(e)-331.6()-6.7(l)-7(l)0(e)-9.2(d)-329.4(w)-7.7(i)0(t)-8.2(h)]TJ
0 -1.1116 TD
[(a)-405.4()45()-6.8(b)-6.9(es)-8.9(t)-404.4(g)0(u)-8(e)-8(s)-6.7(s)44.1()-404.2(s)-6.7(t)-7(a)0(n)-9.1(d)-6.9(ar)-9.1(d)-404.3(r)-6.8(ef)-9.1(e)-8(r)0(e)-9.1(n)-6.9(ce)-407.7(s)-6.7(e)-8(qu)-8(e)-8(n)0(c)-9.1(e)-8(,)-400.8(g)-6.9(iv)-8.1(i)-7(n)0(g)-405.4(t)-7(h)-6.9(o)0(s)-7.8(e)]TJ
T*
.0076 Tc
[(shor)7.6(t)-409.4(r)7.6(ead)7.6(s)-409.1(th)7.6(at)-402.6(fail)7.6(ed)-402.4(to)-402.4(resu)7.6(lt)-402.6(in)-408.2(c)7.6(o)-1.5(nt)7.6(igs)-402.2(a)-409.4(c)7.6(h)-1.5(an)7.6(ce)-403.6(to)-402.4(be)]TJ
T*
0 Tc
[(m)-8.1(a)-8(pp)-8(e)-8(d)-444.6(an)-9.1(d)-444.6(p)-6.9(r)-6.8(o)0(d)-8(u)-6.9(ce)-448(a)-8(d)-6.9(di)-8.1(t)-7(i)-7(o)0(n)-8(a)-8(l)-444.7(co)-9.1(n)-6.9(s)-6.7(en)-9.1(s)-6.7(u)0(s)-451.3(s)0(e)-8.9(q)-6.9(ue)-9.1(n)-6.9(c)0(e)-10.3(.)-446.9(Th)-9.2(e)]TJ
0 -1.1174 TD
[(S)-6.7(H)-7.7(I)-6.8(V)0(E)-10(R)-226.8(p)-6.9(i)-7(pe)-9.1(l)-7(i)0(n)-8.1(e)-226.9(t)-7(h)-6.9(u)-6.9(s)-225.5(c)-8(o)-6.9(mb)-9.2(in)-8.1(e)-8(d)]TJ
/F5 1 Tf
13.495 0 TD
.0069 Tc
[(de)-220(nov)6.9(o)]TJ
/F4 1 Tf
3.3752 0 TD
0 Tc
[(a)-8(s)0(s)-7.6(e)-8(mb)-9.2(l)-7(y)-225.7(a)-8(n)-6.9(d)-225.7(r)-6.8(ea)-10.3(d)]TJ
-16.8702 -1.1116 TD
[(m)-8.1(a)-8(pp)-8(i)-7(n)0(g)-209.5(t)0(o)-209.7(m)0(a)-10.4(x)0(i)-8.1(m)-8.1(i)0(z)-9.2(e)-203.8(a)-8(c)-8(c)0(u)-9.1(r)-6.8(ac)-10.3(y)-202.7(a)-8(n)-6.9(d)-202.7(t)-7(h)0(e)-210.7(l)0(e)-9.2(n)-6.9(gt)-8.1(h)-202.7(o)-6.9(f)-202.7(t)-7(h)-6.9(e)-203.8(g)-6.9(e)0(n)-9.1(o)-6.9(me)]TJ
T*
[(t)-7(h)-6.9(at)-291.5(ca)-10.3(n)-283.3(b)-6.9(e)-284.5(a)-8(s)-6.7(s)0(e)-8.9(m)-8.1(bl)-8.1(e)-8(d)0(.)]TJ
1.0137 -1.1174 TD
[(The)-259.1(consensus)-259.3(sequence)-260.9(of)-255.6(mapped)-257.8(reads)-255.3(was)-258.6(determined)]TJ
-1.0137 -1.1116 TD
[(by)-342(the)-338.7(most)-339.6(frequent)-339.5(read)-340.8(call)-341(at)-337.6(each)-342(site.)-337.4(To)-337.5(mitigate)-341.2(the)]TJ
T*
[(effects)-212.7(of)-209.5(low-level)-209.3(contaminant)-213.1(reads,)-206.9(sites)-208.1(with)-212.9(less)-206.9(than)-207.3(10)]TJ
0 -1.1174 TD
[(mapped)-413.3(reads)-410.8(were)-410.7(classied)-410.5(as)-406.3(undetermin)-9(ed.)-404.2(Consensus)]TJ
0 -1.1116 TD
[(sequences)-204.3(were)-203.4(trimmed)-201.6(to)-198.2(the)-200.4(viral)-202.7(genome)-200.2(from)-201.4(HIV-1)]TJ
/F5 1 Tf
22.7912 0 TD
(gag)Tj
/F4 1 Tf
-22.7912 -1.1116 TD
[(\(p17\))-541.1(to)-538(HIV-1)]TJ
/F5 1 Tf
7.1651 0 TD
(nef)Tj
/F4 1 Tf
1.2326 0 TD
[(.)-539.1(This)-535.4(process)-539.5(yielded)-540.2(consensus)-541.6(se-)]TJ
17.1121 67.9242 TD
[(quences)-322(that)-322.6(were)-318.6(each)-324.7(aligned)-321.3(against)-321.1(a)]TJ
/F5 1 Tf
17.0142 0 TD
[(de)-320.1(novo)]TJ
/F4 1 Tf
3.5365 0 TD
(reference)Tj
-20.5506 -1.1174 TD
[(sequence)-347.3(and)-344.3(a)-342.1(set)-350(of)-342(standard)-345.1(reference)-349.7(sequences,)-351.7(in)-342.2(this)]TJ
0 -1.1116 TD
[(case)-284.2(the)-281.1(Los)-280.8(Alamos)-280.5(HIV-1)-283.7(sequence)-284(compendium)-286.6(2012.)]TJ
7.3823 0 0 6.5614 540.2267 707.5841 Tm
(39)Tj
9.843 0 0 9.843 320.8251 692.277 Tm
[(To)-377.8(construct)-380.9(alignments)-383.4(of)-382.3(HIV-1)-381.6(consensus)-380.3(sequences,)]TJ
-1.0137 -1.1116 TD
[(insertions)-599.6(in)-601.3(consensus)-604.9(sequences)-601.7(were)-600.8(excised)-604.4(if)-601.3(they)]TJ
0 -1.1174 TD
[(were)-393.5(not)-395.1(present)-395.8(in)-394(the)-390.5(standard)-396.9(reference)-401.5(sequences.)-397.8(The)]TJ
0 -1.1116 TD
[(resulting)-523.8(alignment)-526.5(was)-523.5(uncertain)-526.2(in)-520.7(that)-524.2(gap)-522.8(characters)]TJ
T*
[(which)-330.2(ank)-322.2(missing)-331.4(data)-329.4(characters)-333.5(could)-329.3(represent)-330.1(a)-324.8(dele-)]TJ
0 -1.1174 TD
[(tion)-396.3(or)-393.8(a)-393.9(missing)-400.5(nucleotide)-395(as)-400.6(in)-394()50.8(AC-GT-???-ACGT.)41.4()]TJ
0 -1.1116 TD
[(These)-285.3(sites)-288.8(were)-289.8(set)-286.6(to)-284.5(missing)-285.3(nucleotide)-285.6(characters:)-294.4()50.8(AC-)]TJ
T*
[(GT???????ACGT.)41.9()]TJ
/F10 1 Tf
8.9663 0 0 8.9663 310.8472 593.5746 Tm
[(Statistical)-336.1(analysis)-334.5(of)-330.4(factors)-333.2(associated)-337.3(with)-336.5(partial)]TJ
0 -1.2203 TD
[(sequencing)-330.4(failure)]TJ
/F4 1 Tf
9.843 0 0 9.843 320.8251 566.192 Tm
-.0156 Tc
[(To)-310.4(ev)-15.6(a)9.8(l).5(uat)-15.6(e)-301.3(fa)-15.6(c)8.7(t).4(or)-15.6(s)-299.8(a)-.6(s)-15.6(s)11.4(oci)-15.6(a)9.7(ted)-316.2(w)-.3(ith)-316.2(par)-15.6(t)10.9(ial)-316.3(s).8(eq)-15.6(u)11(e)-.6(nci)-15.6(n)10.9(g)-310.4(f)-15.6(a)9.9(i).5(l-)]TJ
-1.0137 -1.1116 TD
-.0159 Tc
[(ure,)-462.8(w)-.6(e)-461.7(focu)-15.9(s)10.9(ed)-460.5(on)-460.5(fou)-15.9(r)-444.3(g)-15.9(e)9.5(nomi)-15.9(c)-445.6(r)-15.9(e)9.6(gion)-15.9(s)-449.9(i).2(n)-460.5(t).2(he)-461.7(unal)-15.9(i)10.4(gned)]TJ
T*
[(cons)-15.9(e)9.7(n).3(su)-15.9(s)-242.5(s).5(eque)-15.9(n)9.5(ces)-253(th)-15.9(a)9.5(t)-247.5(w)-15.9(e)8.7(re)-254.3(ampl)-15.9(i)10.4(ed)-253.1(b).3(y)-253.1(e)-.9(xac)-15.9(t)9.4(ly)-253.1(one)-254.3(of)-253.1(th)-15.9(e)]TJ
0 -1.1174 TD
[(fou)-15.9(r)-219.7(prime)-15.9(r)-220.8(s).5(ets)-235.7(o).3(f)-230.1(t).2(he)-231.3(G)-15.9(a)8.7(ll)-230.2(pr)-15.9(o)10.7(t).2(oco)-15.9(l)]TJ
7.3823 0 0 6.5614 447.5904 537.6755 Tm
-.0162 Tc
(10)Tj
9.843 0 0 9.843 454.6771 533.3101 Tm
-.0156 Tc
[(:)-229.9(r)-15.6(e)9.9(g).6(ion)-229.8(s)-15.6(t)11.1(a)-.6(rt)-15.6(-)10.9(2).6(F)-229.6(b)-15.6(e)9.8(t).5(ween)]TJ
-14.6124 -1.1116 TD
-.016 Tc
[(the)-392.6(s).4(tar)-16(t)-375.4(of)-391.4(the)]TJ
/F5 1 Tf
6.376 0 TD
-.0162 Tc
(gag)Tj
/F4 1 Tf
1.8431 0 TD
-.0158 Tc
[(gene)-392.4(and)-391.3(t).3(he)-392.4(2F)-391.1(primer)-391.2(on)-391.3(ampli)-15.8(c)9.5(o).4(n)-391.3(1).4(,)]TJ
-8.2191 -1.1116 TD
[(regi)-15.8(o)10.7(n)-304.9(1)-15.8(R)9.8(-3F)-310.5(bet)-15.8(w)9.8(een)-310.6(the)-311.8(1).4(R)-305.9(a)-15.8(n)9.6(d)-304.9(3F)-310.5(pr)-15.8(i)10.7(mers)-310.5(o).4(n)-310.6(ampli)-15.8(c)9.5(o).4(n)-310.6(2).4(,)]TJ
0 -1.1174 TD
[(regi)-15.8(o)10.7(n)-304.9(2)-15.8(R)9.8(-4F)-310.5(bet)-15.8(w)9.8(een)-310.6(the)-311.8(2).4(R)-305.9(a)-15.8(n)9.6(d)-304.9(4F)-310.5(pr)-15.8(i)10.7(mers)-310.5(o).4(n)-310.6(ampli)-15.8(c)9.5(o).4(n)-310.6(3).4(,)]TJ
0 -1.1116 TD
-.0155 Tc
[(and)-189.4(r).7(egi)-15.5(o)11(n)-183.6(3)-15.5(R)10.1(-).7(end)-189.4(b).7(et)-15.5(w)10.1(een)-189.4(the)-184.8(3)-15.5(R)-174.2(p).7(r)-15.5(i)11(mer)-189.4(and)-189.4(t).6(he)-184.8(e)-15.5(n)9.9(d)-183.6(o)-15.5(f)-173.2(t).6(h)-15.5(e)]TJ
/F5 1 Tf
23.0907 0 TD
(nef)Tj
/F4 1 Tf
-23.0907 -1.1116 TD
0 Tc
[(g)16.2(e)15(n)16.2(e)-192.3(o)16.2(n)-185.4(am)24.2(p)16.2(l)16.1(i)16.1(c)15(on)-175(4)-185.4(\()0()78.5()0(p)26.6(a)15(r)16.2(t)16.1(ia)25.3(l)-185.5(a)15(mp)25.4(l)16.1(i)16.1(c)15(on)-175(s)16.4(e)0(q)25.4(u)16.2(e)15(n)16.2(ce)24.3(s)16.4(,)13.9()68.1()-191.1(s)16.4(e)15(e)-192.3(F)16.3(i)16.1(g)16.2(.)-187.7(1)0(\))26.6(.)]TJ
1.0137 -1.1174 TD
[(Based)-302.4(on)-307.5(PANGEA-HIV)-311(sequencing)-308.2(failure)-309.7(rates,)-310.7(partial)]TJ
-1.0137 -1.1116 TD
[(amplicon)-502.2(sequences)-503.8(were)-502.9(classied)-502.7(into)-500()50.8(undetermined)48.8()]TJ
T*
[(when)-259.9(more)-266(than)-264.9(80%)-257.8(of)-261.4(nucleotide)-268.3(characters)-264.4(were)-266.8(missing,)]TJ
T*
[(and)-373.1()50.8(determine)-10.2(d)49.7()-375.4(when)-375.1(less)-379.7(than)-374.3(60%)-378.7(of)-376.5(characters)-379.6(were)]TJ
0 -1.1174 TD
[(missing.)-294.5(Ambiguous)-299.9(partial)-298.4(amplicon)-294.9(sequences)-302.2(with)-293.5(20%)]TJ
0 -1.1116 TD
[(40%)-303.9(missing)-302.6(characters)-304.7(were)-307.1(not)-302.9(used)-304.9(in)-301.8(the)-298.3(analy)-8(sis.)-300.2(Mul-)]TJ
T*
[(tivariate)-497.7(logistic)-494.1(regression)-496.8(analysis)-494.8(\(gamlss,)]TJ
7.3823 0 0 6.5614 497.2534 406.2046 Tm
(40)Tj
9.843 0 0 9.843 509.4991 401.8393 Tm
[(R)-491.7(version)]TJ
-20.182 -1.1174 TD
[(3.2.0\))-270.4(was)-275.9(used)-270.3(to)-273(identify)-275.3(covariates)-274.9(that)-276.5(were)-272.5(signicantly)]TJ
0 -1.1116 TD
[(associated)-286.2(with)-282(undetermined)-283.1(partial)-281.1(amplicon)-283.3(sequences.)]TJ
/F10 1 Tf
8.9663 0 0 8.9663 310.8472 357.959 Tm
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